NCCAT Tomography Shortcourse
April 12-14, 2021
SEMC and NCCAT will be offering a 3-day workshop focused on the theory and practice of tomographic methods. Cryoelectron tomography (cryoET) is a powerful new method for directly visualizing macromolecular associations and organization in native cells Traditionally, macromolecular structure determination has been limited to the analysis of isolated molecules and structures. CryoET has the unique ability to visualize macromolecular organization in native cells; it utilizes the intrinsic contrast of frozen cellular material to directly image macromolecules.
Short-course Agenda
April 12, 2021
Day 1: Lectures and Roundtables
12:00-12:05 | Welcome |
12:05-12:50 | Lecture 1 – Intro and overview of ET Wei Dai (Rutgers University) |
12:50-13:35 | Lecture 2 – FIB-SEM Bill Rice (New York University) |
13:35-14:20 | Roundtable 1 – Making windows into cells & Choosing the right in situ target and model system |
14:20-14:45 | Break |
14:45-15:30 | Lecture 3 – Cryo-Applications and sub-tomogram averaging Alex Noble (NYSBC/SEMC) |
15:30-16:15 | Lecture 4 – Automated reconstruction, subtomogram averaging methods & data interpretation Steven Ludtke (Baylor College of Medicine) |
16:15-17:00 | Roundtable 2 – The future of in situ cellular structural biology |
17:00-17:30 | Closing and networking/break out rooms |
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April 13, 2021
Day 2: Practical – Appion Protomo (limited space available)
12:00-12:05 | Welcome |
12:05-13:00 | Roundtable 3 – Introductions and flash talks by short course attendees |
13:00-17:00 | Practical 1 Appion III : Fiducial-less Tomography Practical Alex Noble (NYSBC/SEMC) |
13:00-13:30 Full Overview – Tilt-Series Collection, Appion-Protomo alignment, and Sub-tomogram Processing 13:30-14:00 In-Depth Appion-Protomo Workflow 14:00-14:30 Q&A and Practice! 14:30-15:00 Discussion/Break 15:00-15:10 Overview – Sub-Tomogram Alignment and Dynamo 15:10-15:35 Particle Picking using a Template 15:35-16:00 Membrane, and Filament Picking 16:00-16:30 Sub-Tomogram Alignment, Classification, and tools to transfer to Warp/M/Relion 16:30-17:00 Q&A and Practice! 17:00 End |
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April 14, 2021
Day 3: Practical – EMAN2 (limited space available)
12:00-12:05 | Welcome |
12:05-16:45 | Practical 2 EMAN2 tools, sub-tomogram averaging and annotation Muyuan Chen (Baylor College of Medicine) |
12:05-12:50 Basic user interface and visualization of raw data. 12:50-13:35 Tilt series alignment, tomogram reconstruction and CTF estimation 13:35-14:30 Methods for picking particles from tomograms 14:30-15:00 Break 15:00-16:15 Generating initial model and setting up subtomogram averaging runs 16:15-16:45 Q&A |
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16:45-17:00 | Closing & Wrap up |
*All times EST.
Instructors

Rutgers University

Baylor College of Medicine

New York University

New York Structural Biology Center

Baylor College of Medicine